The old timecode one feels more authentic to me. That timecode at the top justs adds to the experience of the crappy presentation from a foreign bootleg.

As far as the rifftrax audio synced to the DVD, my friend gets every new rifftrax that is of a movie he owns and reauthors his DVDs with the new audio commentary. The Rifftax site has a message board with detailed instructions on how to do this. The hard part is getting the actual audio from the movie low enough that you can still hear it without it being loud enough that it covers up the commentary at the louder parts of the film.